SimRNA: A coarse-grained method for RNA folding simulations and 3D structure prediction

Nucleic Acids Research

Volumn 44, Issue 7, 2015, Pages

  Boniecki, Michal J ^a   Lach, Grzegorz ^a   Dawson, Wayne K ^a   Tomala, Konrad ^a   Lukasz, Pawel ^a   Soltysinski, Tomasz ^a   Rother, Kristian M ^a   Bujnicki, Janusz M ^a  

^a INTERNATIONAL INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; COMPLEX FORMATION; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MONTE CARLO METHOD; PREDICTION; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; RNA BINDING; RNA CONFORMATION; RNA FOLDING; RNA SEQUENCE; RNA STRUCTURE; SEQUENCE ANALYSIS; SIMRNA METHOD; SIMULATION; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; MOLECULAR MODEL;

RNA;

COMPUTER SIMULATION; MODELS, MOLECULAR; MONTE CARLO METHOD; NUCLEIC ACID CONFORMATION; RNA; RNA FOLDING; SEQUENCE ANALYSIS, RNA;

EID: 84965133120     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv1479     Document Type: Article

References (57)

1. Atkins, J.F., Gesteland, R.F., Cech, T.R. (2011) RNA Worlds: From Life's Origins to Diversity in Gene Regulation. Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY.
2. Serganov, A., Patel, D.J. (2012) Molecular recognition and function of riboswitches. Curr. Opin. Struct. Biol., 22, 279-286.
3. Leontis, N., Westhof, E. (2012) RNA 3D structure analysis and prediction. Springer-Verlag, Berlin Heidelberg.
4. Doudna, J.A. (2000) Structural genomics of RNA. Nat. Struct. Biol., 7(Suppl), 954-956.
5. Rother, K., Rother, M., Boniecki, M., Puton, T., Bujnicki, J.M. (2011) RNA and protein 3D structure modeling: similarities and differences. J. Mol. Model, 17, 2325-2336.
6. Rother, M., Rother, K., Puton, T., Bujnicki, J.M. (2011) ModeRNA: a tool for comparative modeling of RNA 3D structure. Nucleic Acids Res., 39, 4007-4022.
7. Rother, M., Milanowska, K., Puton, T., Jeleniewicz, J., Rother, K., Bujnicki, J.M. (2011) ModeRNA server: an online tool for modeling RNA 3D structures. Bioinformatics, 27, 2441-2442.
8. Das, R., Baker, D. (2007) Automated de novo prediction of native-like RNA tertiary structures. Proc. Natl. Acad. Sci. U.S.A., 104, 14664-14669.
9. Parisien, M., Major, F. (2008) The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature, 452, 51-55.
10. Ding, F., Sharma, S., Chalasani, P., Demidov, V.V., Broude, N.E., Dokholyan, N.V. (2008) Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. RNA, 14, 1164-1173.
11. Cao, S., Chen, S.J. (2011) Physics-based de novo prediction of RNA 3D structures. J. Phys. Chem. B, 115, 4216-4226.
12. Sijenyi, F., Saro, P., Ouyang, Z., Damm-Ganamet, K., Wood, M., Jiang, J., SantaLucia, J. (2012) In: Leontis, N and Westhof, E (eds). RNA 3D structure analysis and prediction. Springer-Verlag, Berlin Heidelberg.
13. Cruz, J.A., Blanchet, M.F., Boniecki, M., Bujnicki, J.M., Chen, S.J., Cao, S., Das, R., Ding, F., Dokholyan, N.V., Flores, S.C. et al. (2012) RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction. RNA, 14, 610-625.
14. Boniecki, M., Rotkiewicz, P., Skolnick, J., Kolinski, A. (2003) Protein fragment reconstruction using various modeling techniques. J. Comput. Aided Mol. Des., 17, 725-738.
15. Kolinski, A. (2004) Protein modeling and structure prediction with a reduced representation. Acta Biochim. Pol., 51, 349-371.
16. Zhang, D., Konecny, R., Baker, N.A., McCammon, J.A. (2004) Electrostatic interaction between RNA and protein capsid in cowpea chlorotic mottle virus simulated by a coarse-grain RNA model and a Monte Carlo approach. Biopolymers, 75, 325-337.
17. Ponty, Y., Istrate, R., Porcelli, E., Clote, P. (2008) LocalMove: computing on-lattice fits for biopolymers. Nucleic Acids Res., 36, W216-W222.
18. Jost, D., Everaers, R. (2010) Prediction of RNA multiloop and pseudoknot conformations from a lattice-based, coarse-grain tertiary structure model. J. Chem. Phys., 132, 095101.
19. Lamiable, A., Quessette, F., Vial, S., Barth, D., Denise, A. (2013) An algorithmic game-theory approach for coarse-grain prediction of RNA 3D structure. IEEE/ACM Trans. Comput. Biol. Bioinform., 10, 193-199.
20. Mustoe, A.M., Al-Hashimi, H.M., Brooks, C.L. 3rd (2014) Coarse grained models reveal essential contributions of topological constraints to the conformational free energy of RNA bulges. J. Phys. Chem. B, 118, 2615-2627.
21. Jonikas, M.A., Radmer, R.J., Laederach, A., Das, R., Pearlman, S., Herschlag, D., Altman, R.B. (2009) Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA, 15, 189-199.
22. Sulc, P., Romano, F., Ouldridge, T.E., Doye, J.P., Louis, A.A. (2014) A nucleotide-level coarse-grained model of RNA. J. Chem. Phys., 140, 235102.
23. Cao, S., Chen, S.J. (2005) Predicting RNA folding thermodynamics with a reduced chain representation model. RNA, 11, 1884-1897.
24. Pasquali, S., Derreumaux, P. (2010) HiRE-RNA: A high resolution coarse-grained energy model for RNA. J. Phys. Chem. B, 114, 11957-11966.
25. Xia, Z., Bell, D.R., Shi, Y., Ren, P. (2013) RNA 3D structure prediction by using a coarse-grained model and experimental data. J. Phys. Chem. B, 117, 3135-3144.
26. Bernauer, J., Huang, X., Sim, A.Y., Levitt, M. (2011) Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation. RNA, 17, 1066-1075.
27. Denesyuk, N.A., Thirumalai, D. (2013) Coarse-grained model for predicting RNA folding thermodynamics. J. Phys. Chem. B, 117, 4901-4911.
28. Olson, W.K., Flory, P.J. (1972) Spatial configurations of polynucleotide chains. 3. Polydeoxyribonucleotides. Biopolymers, 11, 57-66.
29. Metropolis, N., Ulam, S. (1949) The Monte Carlo method. J. Am. Stat. Assoc., 44, 335-341.
30. Metropolis, N., Rosenbluth, A.W., Rosenbluth, M.N., Teller, A.H., Teller, E. (1953) Equation of state calculations by fast computing machines. J. Chem. Phys., 21, 1087-1092.
31. Leontis, N.B., Westhof, E. (2001) Geometric nomenclature and classification of RNA base pairs. RNA, 7, 499-512.
32. Zirbel, C.L., Sponer, J.E., Sponer, J., Stombaugh, J., Leontis, N.B. (2009) Classification and energetics of the base-phosphate interactions in RNA. Nucleic Acids Res., 37, 4898-4918.
33. Wadley, L.M., Keating, K.S., Duarte, C.M., Pyle, A.M. (2007) Evaluating and learning from RNA pseudotorsional space: quantitative validation of a reduced representation for RNA structure. J. Mol. Biol., 372, 942-957.
34. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
35. Duarte, C.M., Pyle, A.M. (1998) Stepping through an RNA structure: A novel approach to conformational analysis. J. Mol. Biol., 284, 1465-1478.
36. Yang, H., Jossinet, F., Leontis, N., Chen, L., Westbrook, J., Berman, H., Westhof, E. (2003) Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res., 31, 3450-3460.
37. Shortle, D., Simons, K.T., Baker, D. (1998) Clustering of low-energy conformations near the native structures of small proteins. Proc. Natl. Acad. Sci. U.S.A., 95, 11158-11162.
38. Seetin, M.G., Mathews, D.H. (2011) Automated RNA tertiary structure prediction from secondary structure and low-resolution restraints. J. Comput. Chem., 32, 2232-2244.
39. Das, R., Karanicolas, J., Baker, D. (2010) Atomic accuracy in predicting and designing noncanonical RNA structure. Nat. Methods, 7, 291-294.
40. Miao, Z., Adamiak, R.W., Blanchet, M.F., Boniecki, M., Bujnicki, J.M., Chen, S.J., Cheng, C., Chojnowski, G., Chou, F.C., Cordero, P. et al. (2015) RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures. RNA, 21, 1066-1084.
41. Parisien, M., Cruz, J.A., Westhof, E., Major, F. (2009) New metrics for comparing and assessing discrepancies between RNA 3D structures and models. RNA, 15, 1875-1885.
42. Walen, T., Chojnowski, G., Gierski, P., Bujnicki, J.M. (2014) ClaRNA: a classifier of contacts in RNA 3D structures based on a comparative analysis of various classification schemes. Nucleic Acids Res., 42, e151.
43. Hajdin, C.E., Ding, F., Dokholyan, N.V., Weeks, K.M. (2010) On the significance of an RNA tertiary structure prediction. RNA, 16, 1340-1349.
44. Sharma, S., Ding, F., Dokholyan, N.V. (2008) iFoldRNA: three-dimensional RNA structure prediction and folding. Bioinformatics, 24, 1951-1952.
45. Cruz, J.A., Westhof, E. (2011) Sequence-based identification of 3D structural modules in RNA with RMDetect. Nat. Methods, 8, 513-521.
46. Zirbel, C.L., Roll, J., Sweeney, B.A., Petrov, A.I., Pirrung, M., Leontis, N.B. (2015) Identifying novel sequence variants of RNA 3D motifs. Nucleic Acids Res., 43, 7504-7520.
47. Anfinsen, C.B., Scheraga, H.A. (1975) Experimental and theoretical aspects of protein folding. Adv. Protein Chem., 29, 205-300.
48. Zuker, M., Stiegler, P. (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res., 9, 133-148.
49. Schlick, T., Collepardo-Guevara, R., Halvorsen, L.A., Jung, S., Xiao, X. (2011) Biomolecular modeling and simulation: a field coming of age. Q. Rev. Biophys., 44, 1-38.
50. Saunders, M.G., Voth, G.A. (2013) Coarse-graining methods for computational biology. Annu. Rev. Biophys., 42, 73-93.
51. Rother, K., Rother, M., Boniecki, M., Puton, T., Tomala, K., Lukasz, P., Bujnicki, J.M. (2012) In: Leontis, NB and Westhof, E (eds). RNA 3D structure analysis and prediction. Springer-Verlag, Berlin.
52. Matelska, D., Purta, E., Panek, S., Boniecki, M.J., Bujnicki, J.M., Dunin-Horkawicz, S. (2013) S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA. RNA, 19, 1341-1348.
53. Dzananovic, E., Patel, T.R., Chojnowski, G., Boniecki, M.J., Deo, S., McEleney, K., Harding, S.E., Bujnicki, J.M., McKenna, S.A. (2014) Solution conformation of adenovirus virus associated RNA-I and its interaction with PKR. J. Struct. Biol., 185, 48-57.
54. Flores, S.C., Wan, Y., Russell, R., Altman, R.B. (2010) Predicting RNA structure by multiple template homology modeling. Pac. Symp. Biocomput., 216-227.
55. Sim, A.Y., Levitt, M., Minary, P. (2012) Modeling and design by hierarchical natural moves. Proc Natl Acad Sci USA, 109, 2890-2895.
56. Kim, N., Laing, C., Elmetwaly, S., Jung, S., Curuksu, J., Schlick, T. (2014) Graph-based sampling for approximating global helical topologies of RNA. Proc. Natl. Acad. Sci. U.S.A., 111, 4079-4084.
57. Magnus, M., Matelska, D., Lach, G., Chojnowski, G., Boniecki, M.J., Purta, E., Dawson, W., Dunin-Horkawicz, S., Bujnicki, J.M. (2014) Computational modeling of RNA 3D structures, with the aid of experimental restraints. RNA Biol., 11, 522-536.